(2013) Design and analysis of a tunable synchronized oscillator. Brendan Ryback, Dorett Odoni, Ruben van Heck, et. al. Journal of Biological Engineering. 7:26. LinkSummary: Example of using Lux system to build gene circuits. Built a synchronized transcriptional feedback loop using LuxI and LuxR. Used a positive feedback loop with plus pushing LuxI and negative feedback with an AHL lactonase.

Journal of Cell Biology

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Molecular Biology of the Cell

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Molecular and Cellular Biology

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Nature

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Nature Biotechnology

(2014) Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape. Richard I Sherwood, Tatsunori Hashimoto, and Charles W O’Donnel et al. Nature Biotech. 32:171-179. Link. Summary: Researchers at Harvard have developed a technique known as "Protein Interaction Quantification" that can analyze genome-wide DNAse hypersensitivity data. This technique is a high-throughput version of CHIP-Seq that compares DNAse-seq data to a reference genome. Using machine-learning algorithms that factor the shape of all known transcription factors into the calculations, protein interaction quantification predicts the probability that a specific transcription factor occupies a specific section of the genome. This technique is directly relevant to the Haynes lab as a high-throughput method of probing changes in chromatin architecture.

Nature Methods

Summary: The Weiss group at MIT designed CRISPR-based gene repressors and demonstrated that these could be used to build layered circuits (where the product of one gene controls the expression of another) in mammalian cells. Noteworthy: expression of guide RNAs from synthetic introns.

Public Library of Science Biology (PLoS Biology)

(2013) Polycomb Protein SCML2 Regulates the Cell Cycle by Binding and Modulating CDK/CYCLIN/p21 Complexes. Emilio Lecona, Luis Alejandro Rojas, Roberto Bonasio et al. Public Library of Science Biology (PLoS Biology). 11(12): e1001737: Link. Summary: While most work with the Polycomb group of proteins has involved using chromatin modifications to influence the transcriptional status of cell cycle regulators, this study has discovered a transcription-independent function for human Polycomb group proteins in regulating the cell cycle (being the modulation of the progression of cells from G1 into S phase through interacting with p21 to repress CDK2/CYCE complexes during early G1; this does not interact with the Polycomb complex and highlights a relationship between Polycomb's cellular memory and cell-cycle machinery in mammals). The Haynes lab studies the involvement of Polycomb in maintaining chromatin silencing, so although this is not super relevant to our research, it was the most relevant thing I could find in PLoS and is interesting regardless.

Proceedings of the National Academy of Sciences

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Science

(2014) A Cascade of Histone Modifications Induces Chromatin Condensation in Mitosis. Bryan J. Wilkins, Nils A. Rall1, Yogesh Ostwal et al. Science. 343:77-80. Link. Summary: Examined the driving forces of chromatin hypercondensation during mitosis by inserting ultraviolet light inducible cross-linker amino acids in histone proteins of living yeast to trace interactions of proteins along the cell cycle. Found that H3 S10 phosphorylation leads to recruitment of the histone deacetylase Hst2p which removes an acetyl group from histone H4 lysine 16, allowsing the H4 tail to promote fiber condensation on the surface of neighboring nucleosomes. This series of reactions yields a condensin-independent driving force of chromatin hypercondenation during mitosis (where previously it was thought that metaphase chromosome condensation required the condensin complex to remain undisrupted). Although the chromatin marker being researched in this article is H3S10 rather than our marker of interest in the Haynes lab (H3K27me3) I thought the use of ultra violet light could be relevant to Branden's project (although I'm unsure of the details of his work so this may not be the case).

(2014) Total Synthesis of a Functional Designer Eukaryotic Chromosome. Narayana Annaluru, Héloïse Muller, Leslie A. Mitchell et al. Science. 344:55-58. Link. Summary: Designer eukaryotic chromosome synthesized based on native Saccharomyces cerevisiae chromosome III. This chromosome is functional in S.cerevisiae. All nonessential genes were made to be flanked by loxPsym sites which enabled inducible evolution and genome reduction; this allows for direct evolutionary testing (e.g. max number of nonessential genes that can be modified or deleted without a catastrophic loss of fitness). This chromosome synthesis is a major and exciting step forward in synthetic biology. Authors postulate that it will soon be feasible to engineer new eukaryotic genomes with synthetic chromosomes encoding desired function and phenotypic properties. Another very exciting component of this breakthrough is that it was accomplished by undergraduate students, demonstrating the significant power of open sourced work and brain pooling.

(2013) Genetics Driving Epigenetics. Terrence S. Furey, Praveen Sethupathy. Science. 342:705-706. Link. Summary: I don't think this article needs to be discussed in the meeting, however I thought it was a good (and very short) background on how DNA sequence variation influences epigentics through transcription factor modulated histone tail modificatons and epigenetic mechanisms in general. I would recommend lab members not already familiar with this topic to read it!